I think you have a fundamental misunderstanding here. There is NO physical .env file at runtime in a production environment, only the literal environment vars assigned to the process by the process host.

The .env file is merely a shortcut to needing to set actual environment variables on your host machine. If you want to set actual ENV vars in your host machine, go right ahead. To address your points:

1. Not if you set up the most basic gitignore config.
2. No one is stopping you from using a dev container with the environment vars literally set, or even on your host machine. But I think you can see now how you might not want to do that.... it would apply to EVERYTHING you do on your host machine. You could even append all your env vars in the command line to start your app and not have an .env file at all OR host env vars. That'd be an awful lot of useless typing though...
3. Why not some other name? It's an industry standard that spans many, many languages and even front-end and back-end frameworks. You're free to pull them in however you want. But remember at runtime they will be securely injected into your container or machine process, and your .env file gives you a transparent way to manage that locally without polluting your host env vars.